similar to: cv.glmnet errors

Hi, My apologies for asking this question, but could not find the answer elsewhere. I understand the glmnet package uses Fortran code. For example, the lognet.R file includes the lines of code shown below. But how can I see the Fortran code that is being referenced in the code below? Is that provided somewhere in the package source code? .Fortran("lognet",

Hello R-help list, I have a piece of code written by a grad student here at BU which will segfault when using one data set, but complete just fine using another. Both sets are just text files full of real numbers. It seems like a bug within R. It could be a bug within her data, but again, her data is just a bunch of floats, so her data could be triggering a bug within R. I have tried this

R gurus, I have a data set that looks something like this: Site Species DBH #Vines G PLOC 45.9 4 G ACNE 23.3 1 G ACNE 12.0 0 G FRAM 35.9 5 G AEGL 11.2 2 N PLOC 77.3 12 N JUNI 78.6 7 N ACNE 18.9 1 N ACNE 15.7 3 N ACRU 35.5 4 H ACSA2 24.1 6 H ULAM 35.2 7 There are 730 individual trees (22 species) from four sites in the actual data set. I would like to create a second data frame that

Hello, I got an error message saying Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, : NA/NaN/Inf in foreign function call (arg 5) when I try to analysis a binary trait using glmnet(R) by running the following code library(glmnet) Xori <- read.table("c:\\SNP.txt", sep='\t'); Yori <- read.table("c:\\Trait.txt", sep=',');

Hi, I have problem with GPO and dns/kerberos resolution I do a samba -i -d3 to a log file and started on client: gpupdate /force: lpcfg_load: refreshing parameters from /srv/samba/etc/smb.conf params.c:pm_process() - Processing configuration file "/srv/samba/etc/smb.conf" samba version 4.1.0rc2 started. Copyright Andrew Tridgell and the Samba Team 1992-2013 ... ldb_wrap open of

R gurus, I'm working on data analysis for a small project. My response variable is total vines per tree (median = 0, mean = 1.65, min = 0, max = 24). My predictors are two categorical variables (four sites and four species) and one continuous (tree diameter at breast height (DBH)). The main question I'm attempting to answer is whether or not the species identity of a tree has

Dear R users: Recently, I tried to write a program to calculate cross-validated predicted value. My sources are as follows. However, the R reported an error. Could you please check the sources? Thanks. set.seed(100) x<-rnorm(100) y<-sample(rep(0:1,50),replace=T) dat<-data.frame(x,y) library(rms) fito<-lrm(y~x) preo<-predict(fito) pre<-matrix(NA,nrow=100,ncol=200) for (i in

Dear ecology fellows, I tried to implement Morisita-Horn distance (instead of Bray that is in the current version) in the code for the Simper analysis in vegan. I would be very grateful if someone can check if the code is right. function (comm, group, ...) { if (any(rowSums(comm, na.rm = TRUE) == 0)) warning("you have empty rows: results may be meaningless")

I found other problem in error log (samba -i -d 3) GSS server Update(krb5)(1) Update failed: Miscellaneous failure (see text): Failed to find ADMIN01$@CORMANDOM.INT-CORMAN.BE(kvno 3) in keytab FILE:/srv/samba/private/secrets.keytab (arcfour-hmac-md5) I sent a bug for my problems. best regards St?phane ----------------------------------- St?phane PURNELLE Admin.

Hey, I need some help. I want to obtain a cross validation for a regression model (binary response) but I got an error with CVbinary. Well I did this: fit <- lm(resp ~ PC1 + PC2 + PC3 + PC4 + PC5 + PC6 + PC7 + PC8 + PC9+PC10+PC11+PC12+PC13+PC14+PC15+PC16+PC17+PC18+PC19+PC20+PC21+PC22+PC23+PC24+PC25+PC26+PC27+PC28, data = dexp.cp, family=binomial()) CVbinary(fit) Error in sample(nfolds, m,

Hi All,  I am trying to run cv.glmnet(x,y,family="multinomial", nfolds =4) and I only have 8 observations and the number of features I have is 1000, so my x matrix is 8 by 1000 and when I run the following, I get this error, I am not sure what is causing this problem.  Error in predmat[which, , seq(nlami)] = preds :   number of items to replace is not a multiple of replacement length Can

Hi, I have problem with GPO and dns/kerberos resolution I do a samba -i -d3 to a log file and started on client: gpupdate /force: lpcfg_load: refreshing parameters from /srv/samba/etc/smb.conf params.c:pm_process() - Processing configuration file "/srv/samba/etc/smb.conf" samba version 4.1.0rc2 started. Copyright Andrew Tridgell and the Samba Team 1992-2013 ... ldb_wrap open of

Dear all, I just found this issue: dd1 = c(rep(NaN,82), rep(-1, 144), rep(1, 74)) xx = runmed(dd1, 21) -> R crashes reproducibly in R 3.4.3, R3.4.4 (Ubuntu 14.04/Ubuntu 16.04) With GDB: Program received signal SIGSEGV, Segmentation fault. swap (l=53, r=86, window=window at entry=0xc59308, outlist=outlist at entry=0x12ea2e8, nrlist=nrlist at entry=0x114fdd8, print_level=print_level at

Hi, I have read several threads about memory issues in R and I can't seem to find a solution to my problem. I am running a sort of LASSO regression on several subsets of a big dataset. For some subsets it works well, and for some bigger subsets it does not work, with errors of type "cannot allocate vector of size 1.6Gb". The error occurs at this line of the code: example <-

Hi, I run R on a server via SSH, over a terminal. After loading a specific package, how do I know what functions are in that package? Is there any way to list or display them? tia. -- View this message in context: http://www.nabble.com/Check-functions-in-package-tp24707084p24707084.html Sent from the R help mailing list archive at Nabble.com.

Hi, I created a logistic regression model using the glmnet package. This model is of class "glmnet" or "lognet". I wanted to plot a calibration curve for this model using the calibrate() function from rms package, but the objects used are different, rms requires a fit from lrm(). Is there another function for getting the calibration plot for this glmnet object, or can anyone

>>>>> Hilmar Berger >>>>> on Fri, 5 Oct 2018 10:17:49 +0200 writes: > Dear all, I just found this issue: > I just found this issue: > dd1 = c(rep(NaN,82), rep(-1, 144), rep(1, 74)) > xx = runmed(dd1, 21) >> R crashes reproducibly in R 3.4.3, R3.4.4 (Ubuntu 14.04/Ubuntu 16.04) and also in the latest development version

Hi, I have problem with GPO and dns/kerberos resolution I do a samba -i -d3 to a log file and started on client: gpupdate /force: lpcfg_load: refreshing parameters from /srv/samba/etc/smb.conf params.c:pm_process() - Processing configuration file "/srv/samba/etc/smb.conf" samba version 4.1.0rc2 started. Copyright Andrew Tridgell and the Samba Team 1992-2013 GENSEC backend

Hello fellow R users, I have been getting a strange error message when using the cv.glmnet function in the glmnet package. I am attempting to fit a multinomial regression using the lasso. covars is a matrix with 80 rows and roughly 4000 columns, all the covariates are binary. resp is an eight level factor. I can fit the model with no errors but when I try to cross-validate after about 30 seconds

Dear List, I'm running simulations using the glmnet package. I need to use an 'automated' method for model selection at each iteration of the simulation. The cv.glmnet function in the same package is handy for that purpose. However, in my simulation I have p >> N, and in some cases the selected model from cv.glmet is essentially shrinking all coefficients to zero. In this case,